Re: Help for asking upstreams about free licenses urgently needed (Was: Help: Seeking source code of guppy base caller)
Hi Jun,
On Mon, Apr 27, 2020 at 05:06:41PM +0200, Jun Aruga wrote:
> > this brings up again my point: We *really*, *really* should take the
> > chance right now to ask upstreams for free licensing. The time is good.
> > We just need somebody who is really doing this.
>
> For us, the free licensing is good. But for the company nanopore
> technologies it is their core competency.
> I am not sure we can make it happen, but it might be worth trying to ask.
That's what I mean: Just lets ask (not only in this case but also
in others). There are always good arguments for Open Source and
if nobody asks we will not reach anything. As you can see here
https://wiki.debian.org/DebianMed/SoftwareLiberation
our (partly continuous asking) had quite some success. With COVID-19 we
have one more good reason to ask. I'm simply lacking time and energy to
do *all* this.
> > On Mon, Apr 27, 2020 at 04:21:12PM +0200, Michael Crusoe wrote:
> > > Extracting the linked deb, one finds a binary and a very restrictive
> > > license. I do not believe that guppy source code is available nor it is
> > > likely to become available any time soon.
> > >
> > > While some of their other basecallers have source code available, I would
> > > not call the license OSS:
> > > https://github.com/nanoporetech/flappie/blob/master/LICENCE.txt
>
> I found guppy client software that might be an alternative to use
> guppy's function.
> https://github.com/nanoporetech/pyguppyclient
I have not checked but isn't this just a Python interface to guppy?
> As Michael mentioned, checking other basecallers for nanopore, then
> communicating the nf-core/nanoseq project using the alternative base
> caller optionally.
>
> I found an interesting document about the basecallers.
> https://github.com/rrwick/Basecalling-comparison
I've also found this one.
> Performance of neural network basecalling tools for Oxford Nanopore sequencing
> https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1727-y
>
> > In this study, we tested four basecalling programs developed by ONT – Albacore, Guppy, Scrappie and Flappie
> > ...
> > We also tested Chiron (https://github.com/haotianteng/Chiron), a third-party basecaller still under development that uses a deeper neural network than ONT’s basecallers [3].
>
> The third party basecaller Chiron's license is Mozilla Public License, v. 2.0.
> https://github.com/haotianteng/Chiron/blob/master/LICENSE.md
I have no idea whether we can make this a drop in replacement.
But may be its interesting in any case.
Kind regards
Andreas.
--
http://fam-tille.de
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